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Volumn 25, Issue 2, 2009, Pages 204-210

Identification of structurally conserved residues of proteins in absence of structural homologs using neural network ensemble

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ARTIFICIAL NEURAL NETWORK; COMPUTER PREDICTION; CONTROLLED STUDY; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN STRUCTURE; QUALITY CONTROL; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY; STRUCTURAL PROTEOMICS; STRUCTURE ANALYSIS;

EID: 58349085114     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn618     Document Type: Article
Times cited : (11)

References (31)
  • 1
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 2
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen,C.B. (1973) Principles that govern the folding of protein chains. Science, 181, 223-230.
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 3
    • 0033954256 scopus 로고    scopus 로고
    • The Protein Data Bank
    • Berman,H.M. et al. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
    • (2000) Nucleic Acids Res , vol.28 , pp. 235-242
    • Berman, H.M.1
  • 4
    • 2942522713 scopus 로고    scopus 로고
    • PASS2: An automated database of protein alignments organised as structural superfamilies
    • Bhaduri,A. et al. (2004) PASS2: An automated database of protein alignments organised as structural superfamilies. BMC Bioinformatics 5, 35.
    • (2004) BMC Bioinformatics , vol.5 , pp. 35
    • Bhaduri, A.1
  • 5
    • 3042644660 scopus 로고    scopus 로고
    • Regions of minimal structural variation among members of protein domain superfamilies: Application to remote homology detection and modeling using distant relationships
    • Chakrabarti,S. and Sowdhamini,R. (2003) Regions of minimal structural variation among members of protein domain superfamilies: Application to remote homology detection and modeling using distant relationships. FEBS Lett., 569, 31-36.
    • (2003) FEBS Lett , vol.569 , pp. 31-36
    • Chakrabarti, S.1    Sowdhamini, R.2
  • 6
    • 0345600220 scopus 로고    scopus 로고
    • SMoS: A database of structural motifs of superfamily
    • Chakrabarti,S. et al. (2003) SMoS: A database of structural motifs of superfamily. Protein Eng., 16, 791-793.
    • (2003) Protein Eng , vol.16 , pp. 791-793
    • Chakrabarti, S.1
  • 7
    • 33748933404 scopus 로고    scopus 로고
    • SSToSS - sequence-structural templates of single-member superfamilies
    • Chakrabarti,S. et al. (2006) SSToSS - sequence-structural templates of single-member superfamilies. In Sillico Biol., 6 0029.
    • (2006) In Sillico Biol , vol.6 , pp. 0029
    • Chakrabarti, S.1
  • 8
    • 0027122748 scopus 로고
    • Proteins. One thousand families for the molecular biologist
    • Chothia,C. (1992) Proteins. One thousand families for the molecular biologist. Nature, 357, 543-544.
    • (1992) Nature , vol.357 , pp. 543-544
    • Chothia, C.1
  • 9
    • 0034775160 scopus 로고    scopus 로고
    • Role of conserved residues in structure and stability: Tryptophans of human serum retinol-binding protein, a model for the lipocalin superfamily
    • Greene,L.H. et al. (2001) Role of conserved residues in structure and stability: Tryptophans of human serum retinol-binding protein, a model for the lipocalin superfamily. Protein Sci., 10, 2301-2316.
    • (2001) Protein Sci , vol.10 , pp. 2301-2316
    • Greene, L.H.1
  • 10
    • 0027361123 scopus 로고
    • A structural basis for sequence comparisons. An evaluation of scoring methodologies
    • Johnson,M.S. and Overington,J.P. (1993) A structural basis for sequence comparisons. An evaluation of scoring methodologies. J. Mol. Biol. 233,716-738.
    • (1993) J. Mol. Biol , vol.233 , pp. 716-738
    • Johnson, M.S.1    Overington, J.P.2
  • 11
    • 0032892577 scopus 로고    scopus 로고
    • AAindex: Amino acid index database
    • Kawashima,S. et al. (1999) AAindex: Amino acid index database. Nucleic Acids Res., 27, 368-369.
    • (1999) Nucleic Acids Res , vol.27 , pp. 368-369
    • Kawashima, S.1
  • 12
    • 0000086449 scopus 로고    scopus 로고
    • Negatively correlated neural networks can produce best ensembles
    • Liu,Y. and Yao,X. (1997) Negatively correlated neural networks can produce best ensembles. Aust. J. Intell. Inf. Process. Syst., 4 176-185.
    • (1997) Aust. J. Intell. Inf. Process. Syst , vol.4 , pp. 176-185
    • Liu, Y.1    Yao, X.2
  • 13
    • 0033485370 scopus 로고    scopus 로고
    • Ensemble learning via negative correlation
    • Liu,Y. and Yao,X. (1999a) Ensemble learning via negative correlation. Neural Netw., 12, 1399-1404.
    • (1999) Neural Netw , vol.12 , pp. 1399-1404
    • Liu, Y.1    Yao, X.2
  • 14
    • 0033280266 scopus 로고    scopus 로고
    • Simultaneous training of negatively correlated neural networks in an ensemble
    • Liu,Y. and Yao,X. (1999b) Simultaneous training of negatively correlated neural networks in an ensemble. IEEE Trans. Syst. Man Cybern. B Cybern., 29, 716-725.
    • (1999) IEEE Trans. Syst. Man Cybern. B Cybern , vol.29 , pp. 716-725
    • Liu, Y.1    Yao, X.2
  • 15
    • 0030334834 scopus 로고    scopus 로고
    • Structure of the transition state for folding of the 129 aa protein chey resembles that of a smaller protein, ci2
    • Lopez-Hernandez,E. and Serrano,L. (1996) Structure of the transition state for folding of the 129 aa protein chey resembles that of a smaller protein, ci2. Fold. Des., 1, 43-55.
    • (1996) Fold. Des , vol.1 , pp. 43-55
    • Lopez-Hernandez, E.1    Serrano, L.2
  • 16
    • 0034044314 scopus 로고    scopus 로고
    • The PSIPRED protein structure prediction server
    • McGuffin,L.J. et al. (2000) The PSIPRED protein structure prediction server. Bioinformatics, 16, 404-405.
    • (2000) Bioinformatics , vol.16 , pp. 404-405
    • McGuffin, L.J.1
  • 17
    • 0035957514 scopus 로고    scopus 로고
    • Evolutionary conservation of the folding nucleus
    • Mirny,L. and Shakhnovich,E. (2001) Evolutionary conservation of the folding nucleus. J. Mol. Biol., 308, 123-129.
    • (2001) J. Mol. Biol , vol.308 , pp. 123-129
    • Mirny, L.1    Shakhnovich, E.2
  • 18
    • 0031714858 scopus 로고    scopus 로고
    • JOY: Protein sequence-structure representation and analysis
    • Mizuguchi,K. et al. (1998) JOY: Protein sequence-structure representation and analysis. Bioinformatics, 14, 617-623.
    • (1998) Bioinformatics , vol.14 , pp. 617-623
    • Mizuguchi, K.1
  • 19
    • 0029144601 scopus 로고
    • Gibbs motif sampling: Detection of bacterial outer membrane protein repeats
    • Neuwald,A.F. et al. (1995) Gibbs motif sampling: Detection of bacterial outer membrane protein repeats. Protein Sci., 4, 1618-1632.
    • (1995) Protein Sci , vol.4 , pp. 1618-1632
    • Neuwald, A.F.1
  • 20
    • 23144434732 scopus 로고    scopus 로고
    • CAMPO, SCR_FIND and CHC_FIND: A suite of web tools for computational structural biology
    • Paiardini,A. et al. (2005) CAMPO, SCR_FIND and CHC_FIND: A suite of web tools for computational structural biology. Nucleic Acids Res. 33, W50-W55.
    • (2005) Nucleic Acids Res , vol.33
    • Paiardini, A.1
  • 21
    • 33645831409 scopus 로고    scopus 로고
    • Identification of similar regions of protein structures using integrated sequence and structure analysis tools
    • Peters,B. et al. (2006) Identification of similar regions of protein structures using integrated sequence and structure analysis tools. BMC Struct. Biol., 6, 4.
    • (2006) BMC Struct. Biol , vol.6 , pp. 4
    • Peters, B.1
  • 22
    • 34047122756 scopus 로고    scopus 로고
    • SMotif: A server for structural motifs in proteins
    • Pugalenthi,G. et al. (2007) SMotif: A server for structural motifs in proteins. Bioinformatics. 23, 637-638.
    • (2007) Bioinformatics , vol.23 , pp. 637-638
    • Pugalenthi, G.1
  • 23
    • 38549158429 scopus 로고    scopus 로고
    • MegaMotifBase: A database of structural motifs in protein families and superfamilies
    • Pugalenthi,G. et al. (2008a) MegaMotifBase: A database of structural motifs in protein families and superfamilies. Nucleic Acid Res., 36, D218-D221.
    • (2008) Nucleic Acid Res , vol.36
    • Pugalenthi, G.1
  • 24
    • 38749104235 scopus 로고    scopus 로고
    • Identification of catalytic residues from protein structure using support vector machine with sequence and structural features
    • Pugalenthi,G. et al. (2008b) Identification of catalytic residues from protein structure using support vector machine with sequence and structural features. Biochem. Biophys. Res. Commun., 367, 630634.
    • (2008) Biochem. Biophys. Res. Commun , vol.367 , pp. 630634
    • Pugalenthi, G.1
  • 25
    • 44949092507 scopus 로고    scopus 로고
    • CUSP: An algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations
    • Sandhya,S. et al. (2008) CUSP: An algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations. BMC Struct. Biol., 8, 28.
    • (2008) BMC Struct. Biol , vol.8 , pp. 28
    • Sandhya, S.1
  • 26
    • 0028174103 scopus 로고
    • Identification of sequence motifs from a set of proteins with related function
    • Saqi,M.A. and Sternberg,M.J. (1994) Identification of sequence motifs from a set of proteins with related function. Protein Eng., 7 165-171.
    • (1994) Protein Eng , vol.7 , pp. 165-171
    • Saqi, M.A.1    Sternberg, M.J.2
  • 27
    • 0347994105 scopus 로고    scopus 로고
    • FoldMiner: Structural motif discovery using an improved superposition algorithm
    • Shapiro,J. and Brutlag,D. (2004) FoldMiner: Structural motif discovery using an improved superposition algorithm. Protein Sci., 13, 278-294.
    • (2004) Protein Sci , vol.13 , pp. 278-294
    • Shapiro, J.1    Brutlag, D.2
  • 28
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson,J.D. et al. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1
  • 29
    • 1942502830 scopus 로고    scopus 로고
    • Catalytic and structural role of a metal-free histidine residue in bovine Cu-Zn Superoxide dismutase
    • Toyama,A (2004) Catalytic and structural role of a metal-free histidine residue in bovine Cu-Zn Superoxide dismutase Biochemistry, 43 4670-4679.
    • (2004) Biochemistry , vol.43 , pp. 4670-4679
    • Toyama, A.1
  • 31
    • 0034844341 scopus 로고    scopus 로고
    • Neural network ensembles and their application to traffic flow prediction in telecommunications networks
    • IEEE Press, Washington DC
    • Yao,X. et al. (2001) Neural network ensembles and their application to traffic flow prediction in telecommunications networks. In Proceedings of International Joint Conference on Neural Networks IEEE Press, Washington DC 1, pp. 693-698.
    • (2001) Proceedings of International Joint Conference on Neural Networks , vol.1 , pp. 693-698
    • Yao, X.1


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